The effect of an acute copper exposure on the diversity of a microbial community in North Sea sediments as revealed by DGGE analysis - the importance of the protocol

The aim of the work was to investigate whether the marine bacterial communities in a North Sea sediment with background metal concentrations were affected by an acute copper exposure and if a commonly used molecular technique, denaturing gradient gel electrophoresis (DGGE), was robust enough to investigate the community changes. Sediments (n = 6) were placed in small microcosms and spiked with copper (50 µg/1). Controls were left untreated. After 12 days, bioavailable copper increased up to a factor 2.5 in the sediments. Plate counts and chitinase activity measurements have suggested limited effects of copper on growth rate and cell metabolism. To test the robustness of DGGE three different protocols were used. The three protocols lead to different conclusions. As a whole, it seems that copper had no immediate effect on the genetic diversity of the community. However, copper-sensitive bacterial populations were detected by one of the DGGE protocols. It is concluded that the DGGE approach is a valuable tool to investigate the effect of pollutants on microbial communities only if various DGGE protocols are compared

The archaebacterial communities in Antarctic bathypelagic sediments

16S ribosomal DNA clone library analysis was performed to assess archaeal diversity within three surficial sediment samples obtained from the bathypelagic zone (depth: 2165-3406 in) of the Weddell Sea, Antarctica. The nearly complete 16S rDNA gene (1440bp) was obtained for 146 clones and 46 phylotypes were defined. The majority of the sequences (> 99%) formed three clusters within the Marine Group I Crenarchaeota. The most important cluster, with 78.8% of the clones, included Candidatus Nitrosopumilus maritimus, a mesophilic archaeon able to oxidize ammonia. The most important subgroup in that cluster was the APA4-0cm subgroup (with 62.3% of the clones). This subgroup might represent important Crenarchaeota in the functioning of the bathypelagic sedimentary ecosystems of the Weddell Sea because it dominated the clone libraries in all sampling stations, and was found in sediments separated by very large geographic distances. Only one clone grouped within the Euryarchaeota. This euryarchaeal clone could not be affiliated with any of the previously defined clusters and might represent a novel euryarchaeal lineage

Iron encrustation of the bivalve <i>Montacuta ferruginosa</i>

The epibiotic iron-encrusted biofilms occurring on the shell of the bivalve Montacuta ferruginosa were examined over an annual cycle in order to determine possible variation of the iron-encrustation. Among the 379 examined specimens, well-coated bivalves always predominate. However, it was found that about 50% of the small-sized bivalves were uncoated or weakly coated during the summer months. This result can be explained by the life history of the bivalve and by the physico-chemical conditions in the sediments

The iron-encrusted microbial community of <i>Urothoe poseidonis</i> (Crustacea, Amphipoda)

A rust-coloured coating frequently covers the appendages and sternites of Urothoe poseidonis, an amphipod living in the burrow of the echinoid Echinocardium cordatum. Up to 80% of the collected amphipods were coated. In winter, coated amphipods were always more abundant than uncoated ones. In summer, uncoated specimens predominated. The aspect, location and development of the coating are similar in juveniles and adults. EDAX analyses and Prussian blue testing indicate that the rust-coloured coating contains iron oxyhydroxide minerals with trace metals and phosphorus. Scanning electron microscopy shows that the iron coating harbours bacterial filaments related to Beggiatoaceae (3 morphotypes were observed). Protozoans, possibly Peritrichia of the families Rovinjellidae or Vaginicolidae (one morphotype), were also observed on pereopods VI and VII. The formation of the iron coating and its potential role in the biology of the amphipod are discussed

Bacterial diversity of the sediments transiting through the gut of <i>Holothuria scabra</i> (Holothuroidea; Echinodermata)

This work analyzes bacterial diversity of sediments transiting through the gut of Holothuria scabra which is an important bioturbator in tropical shallow waters. This edible holothurian species has a social and economic importance for coastal populations in many developing countries. Bacterial biodiversity was analyzed by sequencing the 16S rRNA of bacterial cultures and clones. DAPI and FISH methods were used to determine and compare the number of bacteria found in the various gut compartments. A total of 116 phylotypes belonging to the ?-Proteobacteria (60.5 %), a-Proteobacteria (24.5 %), Bacteroidetes (6 %), Actinobacteria (2.75 %), Fusobacteria (1.75 %), Firmicutes (1.75 %), Cyanobacteria (1.75 %) and d-Proteobacteria (1 %) were identified. The number of bacteria is significantly greater (1.5×) in the foregut than in the ambient sediments. The number of bacteria significantly decreases in the midgut and remains stable until defecation. Some ?-Proteobacteria, especially Vibrio, are less affected by digestion than other bacterial taxa. The season has an impact on the bacterial diversity found in the sediments transiting through the gut: in the dry season, ?-Proteobacteria are the most abundant taxon, while a-Proteobacteria dominate in the rainy season. Vibrio is the most frequent genus with some well-known opportunistic pathogens like V. harveyi, V. alginolyticus and V. proteolyticus. Findings show that sediment-associated microbial communities are significantly modified by H. scabra during their transit through the gut which supports the view that holothurians play a substantial role in the structuring of bacterial communities at the sediment–seawater interface

Effect of bacterial mineralization of phytoplankton-derived phytodetritus on the release of arsenic, cobalt and manganese from muddy sediments in the Southern North Sea. A microcosm study

Muddy sediments of the Belgian Continental Zone (BCZ) are contaminated by metals such as Co, As, Cd, Pb, and Ni. Previous studies have suggested that mineralization of phytodetritus accumulating each year on sediments might cause secondary contaminations of the overlying seawater (metal effluxes). The aim of the present research was to investigate these effluxes using a microcosm approach. Muddy sediments were placed in microcosms (diameter: 15cm) and overlaid by phytodetritus (a mix of Phaeocystis globosa with the diatom Skeletonema costatum). The final suspension was 130.6mgL(-1) (dw) and the final chlorophyll a content was 750±35µgL(-1) (mean±SD). Natural seawater was used for controls. Microcosms were then incubated in the dark at 15°C during 7days. Metals were monitored in overlying waters and microbial communities were followed using bacterial and nanoflagellate DAPI counts, thymidine incorporation, community level physiological profiling (CLPP) and fluorescein diacetate analysis (FDA). Benthic effluxes observed in sediments exposed to phytodetritus were always more elevated than those observed in controls. Large effluxes were observed for Mn, Co and As, reaching 1084nmolm(-2)day(-1) (As), 512nmolm(-2)day(-1) (Co), and 755µmolm(-2)day(-1) (Mn). A clear link was established between heterotrophic microbial activity and metal effluxes. The onset of mineralization was very fast and started within 2h of deposition as revealed by CLPP. An increased bacterial production was observed after two days (8.7mgCm(-2)day(-2)) and the bacterial biomass appeared controlled by heterotrophic nanoflagellates. Calculations suggest that during phytoplankton blooms the microbial activity alone may release substantial amounts of dissolved arsenic in areas of the BCZ covered by muddy sediments

Impact of phytoplankton bloom deposition and concomitant metal fluxes on the composition and activity of benthic microbial communities in subtidal marine sediments: A microcosm study

Muddy subtidal sediments in the Belgian Coastal Zone (BCZ, southern North Sea) are characterized by high concentrations of trace metals. During spring, this area is characterized by extensive phytoplankton blooms, which upon sedimentation induce intense remineralization and significant changes in the redox state of the sediments, leading to enhanced trace metal effluxes. We used microcosms to evaluate the interaction between the deposition of moderate concentrations (+ 7.1 mg m-2 of chlorophyll a) of the diatom Skeletonema sp. and the haptophyte Phaeocystis globosa, metal effluxes and microbial community structure and activity. Sediments were sampled after 0, 2 and 7 days. Changes in composition and activity of both the bacterial and microbial eukaryotic communities (with emphasis on Protozoa) were analyzed using molecular methods (16s and 18s rDNA and rRNA extractions followed by DGGE), and related to bacterial biomass, number of heterotrophic nanoflagellates, dissolved metals and other geochemical variables (redox, 02, salinity, pH, chlorophyll and DOC). Gamma-Proteobacteria, Bacteroidetes and delta- Proteobacteria were the dominant bacterial members, while Alveolata (ciliates, dinoflagellates and apicomplexans), diatoms, Fungi, and Amoebozoa were dominant in the microeukaryotic communities. DNA- and RNA-based fingerprints of bacteria and Protozoa showed distinct changes in the total and active community structure as a consequence of the algal enrichment, and with time. The enrichment effect was most pronounced after 2 and 7 days for bacteria and Protozoa respectively. Our results suggest that phytodetritus deposition activates and stimulates the microbial loop, via changes in bacterial activity, biomass and community composition, together with subsequent changes in numbers and relative abundance of heterotrophic nanoflagellates and ciliates, and composition and activity of protozoan communities

Effects of spring phytoplankton bloom deposition on seasonal dynamics and vertical distribution of microbial eukaryotes in a silty, metal-contaminated sediment in the Southern North Sea

Microbial communities from a subtidal, silty, metal-contaminated sediment in the Belgian Coastal Zone, sampled between February and July 2008, were studied using denaturant gradient gel electrophoresis (DGGE). Seasonal and vertical dynamics in the structure of the microeukaryotic community, and Protozoa in particular, were studied in relation to the sedimentation of the spring phytoplankton bloom and linked to variation in the biogeochemical environment, including trace metal dynamics, as previous research had demonstrated that accumulated metals in sediments are released upon bloom sedimentation and degradation (Gao, et al., 2009). Stramenopila (mainly diatoms) were the dominant group in the sediments, followed by Alveolata (ciliates and dinophytes) and Rhizaria (cercozoans, acanthareans and foraminiferans). Sedimentation of the bloom was reflected in increased levels of chlorophyll a and higher abundances of diatoms in the upper sediment layers, and resulted in higher bacterial biomass. Microeukaryote and protozoan community composition changed from February to July, with especially May and July being distinct. Increased microbial mineralization caused pronounced changes in the redox environment and the bioavailable metal concentrations in the sediment, which correlated with the observed seasonal and vertical variation patterns in community structure. Eh and pH were the dominant factors structuring the communities, but trace metals as well had a significant, independent impact on microbial community structure. While no negative effect could be found between the metals and microeukaryotic and protozoan diversity, some taxa, such as a dinoflagellate, appeared to be strongly affected by metal concentrations, while other groups (e.g. ciliates) appeared to be unaffected by higher metal concentrations

Geochemical behavior of trace elements in sub-tidal marine sediments of the Belgian coast

High resolution profiles of trace elements (Fe, Mn, Co, As, Cu, Cr, Ni and Pb) were assessed using the DET (Diffusive Equilibrium in Thin films) and DGT (Diffusive Gradients in Thin films) techniques in silty, organically enriched, sub-tidal sediments of the Belgian coast during late winter and spring 2008. The general chemical properties of the sediments such as dissolved oxygen, pH, Eh and sulfide profiles, controlling precipitation/ mobilization reactions, were determined with electrodes (pH and Eh) and microelectrodes (oxygen) and AgIDGT probes (sulfide). Most trace elements show subsurface maxima and low concentrations beneath 8 cm of depth. The main physicochemical parameters controlling the vertical concentration profiles are dissolved oxygen and redox potential in the surface sediment and sulfide in the deeper sediment layers. Thermodynamic equilibrium calculations have been carried out verifying which solid phases can explain the dissolved trace metal concentrations. Seasonal variations of trace elements have been observed during the sampling period and sedimentation of fresh particulate organic matter (POM) derived from phytoplankton blooms appear to be the main cause of this temporal variability. Flux calculations based on DGT profiles (these fluxes are minimum ones) show that exchange fluxes of trace metals in February are slightly higher than in April. In addition, “DGT pistons” were deployed at the sediment water interface (SWI) to accumulate labile ions from below. This way all labile ions, binding onto the DGT Chelex resin, are pumped out of the porewaters and the solid sediment phase (only the mobile fraction). These results are a direct estimation of the amount of trace elements that can be released from the upper sediment to the water column (in the range of 4.4•10-5 to 0.10 mmol•m-2•d-1 for Co, Pb, Cr, As, Cu, Ni, Fe and Mn)

Response of diffusive equilibrium in thin films (DET) and diffusive gradients in thin films (DGT) trace metal profiles in sediments to phytodetritus mineralisation

Field data from the Belgian Continental Zone showed elevated trace metal concentrations at the sediment–water interface after the occurrence of a phytoplankton bloom. In the present study, laboratory incubation experiments were used to investigate the effect of the phytodetritus remineralisation process on the release of trace metals from contaminated muddy sediments. This remineralisation process was followed by the measurement of chlorophyll-a and dissolved organic carbon levels in the top sediment layers. Two gel techniques, diffusive equilibrium in thin films (DET) and diffusive gradients in thin films (DGT), were used to assess vertical metal profiles in the sediment pore waters and to calculate the metal effluxes. These metal effluxes compared very well with the trace metal concentration variations in the overlying water of the sediment. Much higher effluxes of Mn, Co and As were observed after 2 days of incubation in the microcosms which received additions of phytodetritus. This trend gradually decreased after 7 days of incubation, suggesting that the elevated efflux of trace metals was proportional to the quantity of phytodetritus mineralised at the sediment–water interface. The release of large amounts of toxic elements from the sediments after phytoplankton blooms can therefore potentially affect the marine ecosystem in the Belgian Continental Zone